This means that you don’t have the newer Github App integration installed.
Check if you have “Travis CI” in https://github.com/settings/installations and if it’s enabled for all repositories.
Normally, it’s installed when you grant Travis access to your Github account. So you can revoke grants at https://github.com/settings/applications and sign up at Travis again.
If you are using https://travis-ci.org (you didn’t specify that or give any links so can’t say), you may need to reset Travis integration for each affected project to get the new logic.
You might also need to fully migrate affected projects to https://travis-ci.com at https://travis-ci.com/account/migrate (I had a project that was enabled at both sites; this typically doesn’t work so well).